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SpectrExcel user guide

Install the desktop application, select an assay, and turn supported spectrophotometer files into an Excel file.

Install

Windows

  1. Open GitHub Releases and download spectrexcel-windows-x86_64.exe.
  2. Verify the download source and its checksum against SHA256SUMS on the release before launching it.
  3. Launch the downloaded file. Acknowledge an operating-system warning only after completing those checks.

Linux

  1. Open GitHub Releases and download SpectrExcel-x86_64.AppImage.tar.gz.
  2. Extract the archive, then launch the AppImage. The archive preserves its execute permission.
  3. Ensure the system provides a working X11/GLX OpenGL implementation and host graphics drivers.

If you instead obtain the raw AppImage, enable its execute permission before launching it:

chmod +x SpectrExcel-x86_64.AppImage
./SpectrExcel-x86_64.AppImage

Create your first export

  1. Launch SpectrExcel.
  2. Select the assay that matches your measurement.
  3. Choose the input file or files.
  4. Configure the options shown for that assay.
  5. Optionally enable Include info sheet to record export details.
  6. Select Generate Excel, choose the output .xlsx file, and confirm the export.

The activity area reports file loading, validation errors, and successful exports.

Layouts and chart previews

Open App settings using the gear button and choose Layout. Both layouts are available for every assay:

  • parameters only is the default layout. Select Preview chart after loading your files to open a separate chart dialog.
  • parameters + preview places inputs, parameters, and export controls on the left and a live chart on the right. The chart appears as soon as input files finish loading and updates automatically when you change chart parameters, including axis ranges, reading wavelengths, wavelength correction, or kinetics file order. The Preview chart button is hidden in this layout.

Layout changes apply immediately and are remembered across restarts. Switching layouts preserves loaded files, current parameter values, and kinetics file order; you do not need to reload your files. The header and activity log remain available in both layouts. Scroll the left panel when its controls do not fit.

The preview panel shows an instruction before files are selected, a loading message while data is being prepared, or an error when files or parameters cannot be used. Fix invalid parameters to restore the chart. Choosing a layout does not change the contents of your exported Excel file.

Optional export details

Every assay has an Include info sheet checkbox below the export controls in both layouts. It starts unchecked and remembers your last choice across assays and application restarts. Enable it before generating an Excel file to append an info worksheet.

The worksheet records:

  • The SpectrExcel version and export date and time, including the timezone.
  • Source filenames and SHA-256 hashes identifying the exact input bytes loaded. Full source paths are not included.
  • The assay, settings affecting the export, and processing steps applied, such as wavelength correction or duplicate removal.

The contents follow the application's language; filenames and hashes remain unchanged. Table headers are bold, with an empty row between sections. Measurement tables, charts, and previews are unaffected.

Keep the original input files alongside the Excel file. The info sheet makes results traceable but does not embed the source files. Hashes describe the inputs as loaded, even if the files change before export.

Citation

If you use SpectrExcel in your work, please cite it using the metadata in CITATION.cff. Releases are archived on Zenodo; for reproducibility, cite the DOI of the version you used.

The app's right-aligned footer link shows the installed version's DOI when the startup lookup succeeds. While lookup is pending, offline, or the version is not archived, it shows the all-versions DOI, which resolves to the latest release. Hover over the link to see which citation it represents.

Privacy and network access

Measurement files are processed locally and are not sent to GitHub or Zenodo.

The app automatically contacts GitHub at startup to check for updates, and again when you select Check updates. It also contacts Zenodo at startup to look up the installed version's DOI; version matching happens locally. Both services receive normal connection information, including your public IP address and request headers. There is currently no setting to disable these startup requests. Requested downloads, project links, and DOI links open in your browser.

See the privacy and network disclosure, GitHub Privacy Statement, and Zenodo Privacy Policy.

Kinetics

Use kinetics to follow absorbance changes over time across one or more .KD measurements.

  1. Select one or more .KD files. SpectrExcel initially sorts them naturally by filename.
  2. Use Reorder files when needed. Columns in the Excel file and chart traces follow this order.
  3. Set the reading wavelength and correction wavelength.
  4. Generate the Excel file.

At every time point, SpectrExcel subtracts absorbance at the correction wavelength from absorbance at the reading wavelength. Choose a reference wavelength where your sample does not absorb. This removes a constant baseline offset, not wavelength-dependent scattering.

Each trace starts at zero seconds at its first recorded measurement, not necessarily the start of the reaction. The Excel file contains corrected traces, a comparison chart, and a raw sheet with values before subtraction on the same relative time axis. Reaction rates and rate constants are not calculated.

Binding / titration

Use binding / titration to compare absorbance spectra from binding or titration experiments in a .SD or .txt file and export them for further analysis.

  1. Select one spectra file.
  2. Set minimum and maximum wavelength values for the chart X axis.
  3. Set minimum and maximum absorbance values for the chart Y axis.
  4. Optionally enable wavelength correction and choose a reference wavelength where your sample does not absorb.
  5. Generate the Excel file.

SpectrExcel removes the standard-deviation column, if present. If the input contains two identical halves of repeated spectra, it keeps one copy. The Excel file includes wavelength and absorbance data for every retained spectrum and an overlaid spectrum chart using the selected ranges. Binding constants are not calculated.

Optional correction subtracts absorbance at the selected wavelength from each spectrum. This removes a constant baseline offset, not wavelength-dependent scattering. Correction is off by default. When applied, a separate raw sheet preserves values before subtraction, after the cleanup described above.

Spectrum family

Use spectrum family to export absorbance spectra recorded over time from one .KD file.

  1. Select one .KD file containing complete spectra recorded at successive acquisition times.
  2. Optionally enable wavelength correction and choose a reference wavelength where your sample does not absorb.
  3. Generate the Excel file.

Tables include acquisition times, wavelengths, and all spectra. Charts show every second spectrum, starting with the first, with wavelength on the X axis and absorbance on the Y axis.

Optional correction subtracts absorbance at the selected wavelength from each spectrum. This removes a constant baseline offset, not wavelength-dependent scattering. Correction is off by default. When applied, a separate raw sheet preserves values before subtraction.

File formats

  • .KD: kinetic measurements used by kinetics and spectrum family.
  • .SD: binary absorbance spectra used by binding / titration.
  • .txt: text absorbance spectra used by binding / titration.

Binary files with old and new headers are supported. Spectra span 190-1100 nm. Files still need the expected instrument structure and complete measurement data.

Troubleshooting

Unsupported or corrupt input

Confirm that the selected assay supports the extension and that the instrument export is complete. An unreadable header, missing spectra, or unavailable selected wavelength causes parsing or export to stop.

Linux does not launch the AppImage

For a raw AppImage, run chmod +x SpectrExcel-x86_64.AppImage. If launch still fails, verify X11/GLX, OpenGL, and host graphics drivers.

Linux file picker is unavailable

Install Zenity or KDialog. SpectrExcel tries Zenity first and KDialog second; without either tool, the system file picker cannot open.

Download or update verification

Use only GitHub Releases. Compare the downloaded file with the published SHA256SUMS checksums before accepting an OS warning or replacing an existing installation.